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Fluorine in PDB 5w2w: Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

Enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

All present enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid:
3.2.1.18;

Protein crystallography data

The structure of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w2w was solved by V.A.Streltsov, J.Mckimm-Breschkin, S.Barrett, P.Pilling, S.Hader, A.G.Watt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.30 / 1.85
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.709, 180.709, 180.709, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.1

Other elements in 5w2w:

The structure of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid (pdb code 5w2w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w2w:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5w2w

Go back to Fluorine Binding Sites List in 5w2w
Fluorine binding site 1 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:70.9
occ:0.80
 FAJ A:9SP501 0.0 70.9 0.8
CAV A:9SP501 1.3 68.0 0.8
OAM A:9SP501 2.2 75.1 0.8
CAO A:9SP501 2.3 54.9 0.8
CAS A:9SP501 2.4 71.6 0.8
FAI A:9SP501 2.5 70.6 0.8
OAC A:9SP501 3.0 50.3 0.8
OAE A:9SP501 3.0 49.4 0.8
CAU A:9SP501 3.6 70.6 0.8
CAR A:9SP501 3.7 64.3 0.8
CAT A:9SP501 4.1 67.9 0.8
CAQ A:9SP501 4.6 66.8 0.8
OAG A:9SP501 4.6 72.9 0.8
OAF A:9SP501 4.7 59.0 0.8
CAP A:9SP501 4.9 57.6 0.8

Fluorine binding site 2 out of 4 in 5w2w

Go back to Fluorine Binding Sites List in 5w2w
Fluorine binding site 2 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:70.6
occ:0.80
 FAI A:9SP501 0.0 70.6 0.8
CAS A:9SP501 1.4 71.6 0.8
CAV A:9SP501 2.4 68.0 0.8
CAR A:9SP501 2.4 64.3 0.8
FAJ A:9SP501 2.5 70.9 0.8
OAF A:9SP501 2.7 59.0 0.8
OAM A:9SP501 3.1 75.1 0.8
CAT A:9SP501 3.2 67.9 0.8
CAO A:9SP501 3.7 54.9 0.8
CAU A:9SP501 3.7 70.6 0.8
OAE A:9SP501 4.1 49.4 0.8
NAL A:9SP501 4.5 55.1 0.8
OD1 A:ASN399 4.7 39.0 1.0
OAG A:9SP501 4.7 72.9 0.8
OAC A:9SP501 4.7 50.3 0.8
CAQ A:9SP501 4.9 66.8 0.8

Fluorine binding site 3 out of 4 in 5w2w

Go back to Fluorine Binding Sites List in 5w2w
Fluorine binding site 3 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F516

b:24.4
occ:0.40
 F1 A:9SD516 0.0 24.4 0.4
F1 A:9S7517 0.8 25.2 0.6
C3 A:9SD516 1.4 22.3 0.4
C3 A:9S7517 2.1 20.0 0.6
C2 A:9SD516 2.3 21.7 0.4
C4 A:9SD516 2.4 21.6 0.4
OD1 A:ASP151 2.4 23.1 1.0
O4 A:9SD516 2.6 21.8 0.4
CG A:ASP151 2.7 24.1 1.0
OD2 A:ASP151 2.8 27.5 1.0
C4 A:9S7517 2.9 18.4 0.6
O4 A:9S7517 2.9 18.7 0.6
C1 A:9SD516 3.0 21.5 0.4
C5 A:9SD516 3.0 21.9 0.4
O1A A:9SD516 3.0 21.7 0.4
C2 A:9S7517 3.1 20.1 0.6
O A:HOH998 3.2 44.5 1.0
C5 A:9S7517 3.2 20.1 0.6
O A:HOH847 3.2 31.4 1.0
O1A A:9S7517 3.2 20.0 0.6
C1 A:9S7517 3.2 20.6 0.6
O6 A:9SD516 3.3 21.3 0.4
O6 A:9S7517 3.3 19.9 0.6
NH1 A:ARG118 3.4 18.1 1.0
O A:HOH618 3.6 20.4 1.0
OE2 A:GLU119 3.6 17.6 1.0
C6 A:9SD516 3.8 21.9 0.4
O A:HOH691 3.8 22.3 1.0
CB A:ASP151 3.8 21.4 1.0
C6 A:9S7517 3.9 18.8 0.6
O1B A:9SD516 4.1 21.3 0.4
O1B A:9S7517 4.1 19.5 0.6
N5 A:9SD516 4.3 22.1 0.4
OH A:TYR405 4.4 20.7 1.0
CZ A:ARG118 4.4 18.0 1.0
O7 A:9S7517 4.4 21.4 0.6
N5 A:9S7517 4.5 19.1 0.6
O A:HOH909 4.5 21.9 1.0
NH2 A:ARG118 4.7 17.8 1.0
CD A:GLU119 4.7 18.4 1.0
O10 A:9SD516 4.7 22.5 0.4
CA A:ASP151 4.8 22.3 1.0
C7 A:9S7517 4.8 21.3 0.6
O7 A:9SD516 4.9 25.8 0.4
C10 A:9SD516 4.9 22.1 0.4
C7 A:9SD516 5.0 23.3 0.4

Fluorine binding site 4 out of 4 in 5w2w

Go back to Fluorine Binding Sites List in 5w2w
Fluorine binding site 4 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Influenza Virus Neuraminidase N9 in Complex with 8-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F517

b:25.2
occ:0.60
 F1 A:9S7517 0.0 25.2 0.6
C3 A:9SD516 0.6 22.3 0.4
F1 A:9SD516 0.8 24.4 0.4
C3 A:9S7517 1.4 20.0 0.6
C2 A:9SD516 1.6 21.7 0.4
C4 A:9SD516 1.9 21.6 0.4
C2 A:9S7517 2.3 20.1 0.6
C4 A:9S7517 2.4 18.4 0.6
C1 A:9SD516 2.4 21.5 0.4
O4 A:9SD516 2.6 21.8 0.4
C1 A:9S7517 2.6 20.6 0.6
O1A A:9SD516 2.6 21.7 0.4
O6 A:9S7517 2.7 19.9 0.6
O1A A:9S7517 2.7 20.0 0.6
O6 A:9SD516 2.7 21.3 0.4
C5 A:9SD516 2.7 21.9 0.4
O4 A:9S7517 2.8 18.7 0.6
C5 A:9S7517 2.8 20.1 0.6
C6 A:9SD516 3.2 21.9 0.4
OD1 A:ASP151 3.2 23.1 1.0
C6 A:9S7517 3.3 18.8 0.6
O A:HOH847 3.4 31.4 1.0
NH1 A:ARG118 3.4 18.1 1.0
OD2 A:ASP151 3.4 27.5 1.0
CG A:ASP151 3.5 24.1 1.0
OH A:TYR405 3.5 20.7 1.0
O1B A:9S7517 3.5 19.5 0.6
OE2 A:GLU119 3.6 17.6 1.0
O1B A:9SD516 3.6 21.3 0.4
O A:HOH998 3.6 44.5 1.0
N5 A:9SD516 4.0 22.1 0.4
O A:HOH618 4.1 20.4 1.0
N5 A:9S7517 4.2 19.1 0.6
CZ A:TYR405 4.2 20.0 1.0
CZ A:ARG118 4.2 18.0 1.0
O7 A:9S7517 4.2 21.4 0.6
NH2 A:ARG118 4.3 17.8 1.0
C7 A:9S7517 4.4 21.3 0.6
CB A:ASP151 4.5 21.4 1.0
O A:HOH691 4.5 22.3 1.0
CD A:GLU119 4.6 18.4 1.0
C7 A:9SD516 4.6 23.3 0.4
O7 A:9SD516 4.7 25.8 0.4
CE2 A:TYR405 4.8 18.5 1.0
O10 A:9SD516 4.8 22.5 0.4
C10 A:9SD516 4.9 22.1 0.4
CE1 A:TYR405 4.9 19.8 1.0
O A:HOH820 4.9 46.6 1.0

Reference:

J.L.Mckimm-Breschkin, S.Barrett, P.A.Pilling, S.Hader, A.G.Watts, V.A.Streltsov. Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-Acetylneuraminic Acid Derivatives. J. Med. Chem. V. 61 1921 2018.
ISSN: ISSN 1520-4804
PubMed: 29397718
DOI: 10.1021/ACS.JMEDCHEM.7B01467
Page generated: Tue Jul 15 08:47:25 2025

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